Gel electrophoresis is capable of separating macromolecules such as proteins and nucleic acids on the basis of size, charge, and/or conformation. Most applications involve the use of a single pair of electrodes to generate the electric field. Such a field is necessarily constrained to be uniform and oriented in a single direction, and as a result conventional techniques are limited in many respects.
For example, conventional electrophoresis is not capable of resolving DNA fragments much larger than 50 kilobases. The recent introduction of new electrode configurations which generate electric fields in alternating orientations has allowed the separation of large DNA molecules up to 2 megabases in size. For example, U.S. Pat. No. 4,473,452 describes an electrophoresis method of separating DNA molecules which involves the use of electric fields deliberately chosen to be nonuniform, rather than the uniform fields sought in previously known electrophoresis methods. The nonuniformity of the electric field, however, causes the DNA molecules to migrate with a mobility and a trajectory that depends on where in the gel the sample is loaded. Thus, comparison of multiple samples across the gel is difficult.
For example, conventional electrophoresis may produce distortion, with molecules at the edge of the gel migrating more slowly than those in the center. Consequently electrophoresis is often done inefficiently at voltages lower than necessary to achieve adequate resolution.
For example, conventional electrophoresis is limited in resolution by band broadening.
Also, conventional electrophoresis is not capable of identifying macromolecules with different secondary structure. Two dimensional electrophoresis has been developed for this purpose, but this method is technically difficult because it involves manipulations of the gel.